Genetics

Question 1

DNA in proks vs euks

Answer 1

single chrm that’s supercoiled and attached to RNA-protein core, in nucleoid/cyto, can also have plasmids vs mult chrms in nucleus/mito/chloroplasts, DNA binds to histones => chromatin

Question 2

Gene expression requires what 2 processes?

Answer 2

transcpxn/RNA synthesis and transln/protein synthesis; regulation of gene expression determines which proteins are synthesized

Question 3

Nucleosides vs nucleotides

Answer 3

pentose + nitrogenous base at C1 vs pentose + nitrogenous base at C1 + phosphate(s) at C5 (alpha/beta/gamma phosphates)

Question 4

Ribose vs deoxyribose

Answer 4

Has -OH at C2 vs has -H at C2

Question 5

Leon Heppel vs Watson and Crick

Answer 5

proved that inorganic phosphate joined w/ nucleotide monomers in early 1950s; nucleotide monomers join by alpha phosphate via phosphodiester bond –> beta and gamma phosphates = cleaved off vs DNA = antiparallel double helix w/ 2 polynucleotide strands joined by base pairing

Question 6

describe double helix

Answer 6

B FORM (right handed helix); stabilized by H bonds, vdw interactions, hydrophobic effect; major grove/big gap, minor groove/little gap; net neg charge b/c 3rd -OH group of phosphate = free

Question 7

what can heat vs alkali do to DNA?

Answer 7

both denatures double helix. converts dsDNA to ssDNA => melting; if temp dec –> reannealing/renaturation/hybridization vs double helix separates but not break phosphodiester bonds (it does in RNA)

Question 8

doxorubicin vs azithromycin vs ciprofloxacin vs melanomas

Answer 8

intercalates b/w base pairs –> inhibits replication and transcpxn; stops/slows growth of ca cells vs inhibits protein synthesis on prok 50S ribosomal subunit (euks don’t have 50S) vs inhibits bacterial DNA gyrase –> inhibits bacterial DNA synthesis (euks have linear DNA and don’t have DNA gyrase) vs UV causes pyrimidine dimers –> mutation from nonrepair of dimers

Question 9

describe chromatin

Answer 9

DNA + nucleosome = chromatin; 2 molec of H2A/H2B/H3/H4 make up core, H1 binds to linker DNA b/w nucleosome beads; when strings of nucleosomes wind into helical and tubular coils => solenoid structure/polynucleosome/30nm-fiber

Question 10

know diff b/w D/RNA

Answer 10

look at the table in Lecture 1

Question 11

mRNA vs rRNA vs tRNA

Answer 11

contains nucleotide seq that’s converted to aa seq of protein; in proks: generated from operon as polycistronic transcript and transcribed; in euks: pre-mRNA processed in nucleus to mature monocistronic mRNA and then leaves nucleus to cytosol vs subcellular ribonucleoprotein complexes where protein synthesis occurs vs carry aa to ribosomes; cloverleaf (3 loops), 2nd loop has anticodon, 3’ end has aa attachment site

Question 12

what # is mito ribosome?

Answer 12

55S (similar to 70S in bacteria)

Question 13

what are the exceptions to central dogma?

Answer 13

viruses have either D/RNA and need hosts to replicate; genetic material = protected by protein coat, protein coat protected by lipid envelope. RETROVIRUSES - have reverse transcriptase to go from RNA to DNA

Question 14

know diff b/w proks/euks

Answer 14

there’s a summary table in Lecture 1

Question 15

origin of replication (ori)

Answer 15

includes short AT-rich segments where DNA synthesis occurs; proks have one ori, euks have mult ori; dsDNA unwinds and separates –> 2 rep forks in opposite directions => bidirectional

Question 16

major players of DNA separation for replication

Answer 16

DNA helicase; single stranded DNA binding proteins - prevent strands from reassociating and protect strands from enzymatic cleavage (ex: RPA); DNA topoisomerase - removes pos and neg supercoils (ex: DNA gyrase)

Question 17

describe the enzymes involved in DNA synthesis

Answer 17

primase makes RNA primer and pol α adds a couple bases and leaves (they also start Okazaki fragments) –> pol ε adds nucleotides on leading strand, pol δ adds nucleotides on lagging strand (stops adding when reaching start of next frag); both proofread (3’-5’ exonuclease activity then 5’-3’ endonuclease activity) –> flap endonuclease 1 (FEN1) and RNAse H remove RNA primers via 5’-3’ exonuclease activity –> pol δ fills in gap from RNA primer –> DNA ligase glues frags together

Question 18

primase for proks vs euks

Answer 18

DnaG vs pol α

Question 19

telomeres vs telomerase vs telomere shortening

Answer 19

complex of noncoding NA + protien at end of linear euk chrm –> maintain structural integrity of chrm; tandem rpts of noncoding hexameric seq: TTAGGG vs maintain telomeric length in germ/stem/ca cells; acts as reverse transcriptase; short RNA seq template => Terc; resolves senescence; look at pic in Lecture 2 vs can lead to senescence which can be good b/c reduce mutation risk

Question 20

what happens if cells can’t repair dmged DNA?

Answer 20

1. senescence or irreversible dormancy
2. apop
3. malignant uncontrolled cell division

Question 21

somatic mutations vs germline/genetic mutations

Answer 21

in cells not involved in gamete prod, no change in phenotype, basis of most ca vs in cells involving gametes –> hereditary

Question 22

sources of DNA dmg

Answer 22

exogenous/environ: ionizing rad like UV and xrays, chemicals like DNA alkylating agents and procarcinogens vs endogenous: hydrolysis rxns (depurination, depyrimidation), [O] of bases –> ROS, mutations in S phase

Question 23

3 major mechanisms for ssDNA repair: nucleotide excision repair vs base excision repair vs mismatch repair

Answer 23

LOCAL distortions of DNA helix –> nuclear endonucleases recognize and cleave abnl chain on 3’ & 5’ side of distorted region –> short oligonucleotide w/ distortion = released –> gap in DNA –> DNA pol and ligase fill in gap (ex: repair pyrimidine dimers) vs DNA lesions involving base alterations or spontaneous loss –> specific glycosylases cleave base –> apurinic/pyrimidinic site (AP site) –> AP endonucleases recognize missing base and make endonucleolytic cut on 5’ side –> deoxyribose phosphate lyase removes the sugar/phosphate hanging out –> DNA pol and ligase complete repair vs non-dmged mismatched bases after DNA pol proofreading error/slip –> in proks: find degree of methylation, in euks: find nicks in strands and how Mut proteins interact w/ PCNA –> endonuclease cuts into strand –> exonuclease removes mismatched bases –> DNA pol and ligase complete repair

Question 24

xeroderma pigmentosum (XP) vs cockayne syndrome & trichothiodystrophy

Answer 24

d/o of NER –> ability to fix DNA dmg from UV = deficient –> freckles & most likely skin ca; children of the night vs d/o in NER and transcpxn-coupled repair from mutations in ERCC6 or ERCC8 genes caused by UV, chemicals, free rad –> NO skin ca, fail to thrive, premature aging

Question 25

microsatellite instability (MSI)

Answer 25

caused by mutations in MMR genes; if inherited --> predisposed to hereditary nonpolyposis colorectal ca (HNPCC); test for MSI = diagnostic for colon ca. microsatellite = short tandem rpts that can tell you if mutations are occurring elsewhere

Question 26

double stranded break repair vs homologous recombination vs non-homologous end joining

Answer 26

hazardous forms of DNA dmg leading to genome rearrangement, mutations and cell death; 2 repair mechanisms: HR and NHEJ but defects in these repair mechanisms --> genetic dz vs only used when homologous DNA = present; BRCA1 and BRCA2 w/ RAD51 maintain strand invasion --> homologous DNA frag restore dmged DNA --> error free vs don't need homologous template --> protein KU recognizes and binds exposed ends => directly join broken ends --> imprecise repair b/c you lose the nucleotides from orig DNA strand

Question 27

Ataxia Telangiectasia (AT) vs Burkitt's Lymphoma

Answer 27

defect in ATM kinase --> doesn't activate checkpoints in response to DNA dmg (usually they help cells recognize dmged or broken DNA strands and coordinate repair) --> inc risk of leukemias and lymphomas. sxs: telangiectasia (broken blood vessels), ataxia (progressive neuro impairment and difficulty coordinating movement) vs caused by c-myc gene classic t reciprocal translocation and deregulation on chrm 8; c-myc = transcriptional activator (proto-oncogene) that affects diff pathways for regulating cell cycle, growth, adhesion, differentiation, and apop; overexpression —> deregulation of cell cycle control

Question 28

missense vs frameshift mutation

Answer 28

single base = diff --> diff aa vs insertion/deletion of single base changes reading frame

Question 29

diff mods after transcribing pre-mRNA

Answer 29

splicing, reading frame, polyadenylation, RNA editing (ex: RNA editing of glutamate receptor by changing adenosine to inosine), RNA export, RNA localization

Question 30

centromere. meta vs submeta vs acrocentric centromere

Answer 30

separates chrms into P and Q arm; based on P arm size compared to Q arm. mid vs a little higher than mid vs very high --> smallest P arm

Question 31

idiogram vs karyotype

Answer 31

drawing of chrms vs photograph of chrms from light microscopy arranged in order; stains during metaphase; use to analyze 5mil bp

Question 32

which chrms are acrocentric?

Answer 32

13-15, 21-22 = AUTOSOMAL ACROCENTRIC

Question 33

G banding. advantages vs disadvantages

Answer 33

geimsa stain; stains AT rich --> less and darker, GC rich --> more and lighter. see large abnlities, easy to perform, reliable vs can't see small abnlities

Question 34

why use karyotype? when?

Answer 34

problems w/ early growth/development, fertility problems, neoplasia, high risk pregnancy. >5mil bp

Question 35

X activation/Lyonization

Answer 35

random epigenetic inactivation of 1 copy of X chrm in females --> Barr body formation; depends on XIST found in X inactivation center (XIC) (no XIC --> no inactivation --> show both X chrms)

Question 36

SRY gene vs pseudoautosomal regions

Answer 36

present on Y chrm; testis-determining factor; males = hemizygous b/c only have 1 Y gene; if SRY gene on XX --> female w/ testis, if SRY gene not on XY --> male w/ no testes vs PAR1 and PAR2: homologous seq found on sex chrms

Question 37

prophase and prometaphase. know MAT as well

Answer 37

nuclear envelope break down, microtubules attach to centromere, chrms start to condense

Question 38

prophase I vs metaphase I vs anaphase I vs telophase I

Answer 38

chrm coil and form a bridge --> synapsis of homologs => synaptonemal complex --> crossing over --> inc genetic variation vs random alignment of bivalents --> indep assortment --> inc genetic variation vs homologous chrms move to opposite sides but sister chromatids still attached at centromere vs cell division, chrms uncoil, nuclear membrane reforms --> cytokinesis but NO DNA replication for meiosis II

Question 39

chromosomal abnlities: numerical vs structural

Answer 39

euploid = exact correct #, aneuploid = abnl # like trisomy or monosomy, polyploidy = have more than 2 complete sets of chrms (>2n) like triploidy (caused by fertilization of 1 egg + 2 sperm => dispermy, or failure of meiosis --> diploid egg/sperm --> miscarriage)

Question 40

meiotic nondisjunction I vs II

Answer 40

gametes have 2 whole chrms 21 or none vs gametes have 2 copies of chrm 21 or none. check Lecture 9 Slide 10

Question 41

numerical: mosaicism vs chimera

Answer 41

1 zygote to 2+ pop of cells in 1 individual; caused by mitotic error/mutation in embryo development (gain/lose chrm by nondisjunction); somatic: symptomatic but not inheritable, germinal: asymptomatic but heritable vs 2 zygotes in 1 individual (dizygotic fraternal twins --> 1 twin absorbs dead twin)

Question 42

numerical: autosomal aneuploidy: trisomy 21 vs 18 vs 13

Answer 42

palmar crease, intellectual disability, congenital heart dz and leukemia vs 1/6000, rarely live past 1st year, clenched fist w/ 2nd and 5th digits overlapping 3 & 4 vs 1/8000, die w/in first days/weeks, polydactyly, cleft palette, cutis aplasia (missing parts of scalp)

Question 43

numerical: sex chrm aneuploidy: XXY vs XO vs XXX vs XYY

Answer 43

tall, hypogonad b/c low testosterone --> infertile, but fairly nml vs short, amenorrhea --> infertile, webbed neck vs tall, increased risk of learning disabilities, but phenotypically nml vs associated w/ acne and learning disabilities, but phenotypically nml

Question 44

structural abnllities can be balanced vs unbalanced

Answer 44

don't lose genetic info --> asx but inheritable vs lose genetic info --> symptomatic (ex: deletion, duplication)

Question 45

structural: deletion vs duplication vs isochrome vs translocation vs inversion

Answer 45

gene = inactivated/deleted and remaining fxnal copy of gene = not adeq to preserve nml fxn --> haploinsufficiency; can result in monosomy depending on size (ex: William's syndrome = del of 7q11.23, elastin/ELN gene in this region --> affects elastic fibers and connective tissue: DiGeorge's syndrome) vs can result in trisomy depending on size (ex: cat-eye syndrome: cardiac defects, cleft palate, skel and kidney problems, hernias, intellectual disability) vs chrm where 1 arm = lost --> other arm = duplicated in mirror fashion; 3 copies of 1 arm = partial trisomy, 1 copy of 1 arm = partial monosomy vs when chrm breaks into frag and frags reattach and diff locations --> still balanced; Robertsonian - joining long arms of acrocentric chrms --> balanced b/c p arms only have rRNA, Reciprocal - exchanging 2 chrm segs b/w 2 chrms --> even and balanced vs 2 breaks in 1 chrm that could be in one arm/doesn't include centromere => paracentric or 1 in each arm/include centromere => pericentric

Question 46

aminoacyl-tRNA synthetase

Answer 46

attaches correct aa to correct tRNA, requires ATP; enzyme has proofreading ability

Question 47

genetic code

Answer 47

specific, universal (specificity = conserved since early stages of evolution), degenerate/redundant (1 aa can have mult codons)

Question 48

IRES. how are viruses involved?

Answer 48

initial ribosome entry site - shunts ribosome to second AUG and begin second transln. when cells = stressed --> transln shuts down --> virus use their IRES to start viral transln while host transln = down

Question 49

cap dep vs indep activation

Answer 49

when cells = stressed (hypoxia, infxn, apop, oncogenes): dec vs inc; uses IRES

Question 50

sickle cell anemia

Answer 50

periodic episodes of pain => crises; sickled-shape RBC block blood flow, break apart easily and die --> anemia, can't carry enough O2 --> fatigue, dmgs spleen; protective against malaria => heterozygote advantage

Question 51

gain of fxn vs loss of fxn vs dominant neg mutation

Answer 51

mutation resulting in new, increased, or unregulated activity for protein; can be frameshift; can be deleterious vs mutation resulting in lost activity for protein; can be frameshift; can be deleterious vs mutation resulting in lost activity and shuts down activity of unmutated proteins

Question 52

DNA polymerase vs heat stable DNA polymerase vs DNA ligase vs RNA polymerase vs Reverse Transcriptase

Answer 52

adds bases from 5' to 3' direction vs a class of DNA polymerases isolate from thermophilic bacteria --> remains active at high temps; Taq DNA polymerase = most common for PCR and cycle sequencing vs forms phosphodiester bond b/w 2 DNA strands; used in cloning vs makes RNA molec complementary to DNA template vs makes DNA molec complementary to RNA template; used for cDNA prod and identifying transcriptional start sites of genes

Question 53

What are restriction enzymes/restriction endonucleases?

Answer 53

Enzymes that recognize SPECIFIC dsDNA 4-8bp seq, particularly palindromic —> once they find the seq, they cleave the phosphodiester bond of DNA backbone; they yield sticky or blunt ends. Used in cloning and some diagnostic assays

Question 54

techniques for amplifying DNA: cloning vs DNA libraries vs PCR

Answer 54

take DNA you want amplified (foreign DNA) and attach it to vector (carrier DNA) --> introduce foreign DNA+carrier DNA to host cell --> host cell replicates its own DNA and foreign+carrier DNA; vectors can be bacteria host (transformed cells) like plasmids/bacteriophage/cosmids or euk host (transfection or transduction) like free DNA/DNA coated w/ lipid layer (liposome)/retro or adenoviruses (transduction-virus)

Question 55

Genomic libraries vs cDNA libraries

Answer 55

Large DNA fragments contains both coding and noncoding genes —> can’t be used for recombination vs small DNA fragments containing coding genes aka exons —> can be used for recombination; made from reverse-transcribing mRNAs

Question 56

Know ab and ag for ABO

Answer 56

Memorize the table in Lecture 10, Slide 4

Question 57

Mendelian d/o and types

Answer 57

genetic d/o caused by single genetic locus. autosomal dom/rec, X-linked dom/rec, Y-linked, mitochondrial

Question 58

Know pedigrees. How to know if auto rec vs auto dom vs x linked rec vs x linked dom

Answer 58

Lecture 10, Slide 7. both M/F, rare vs both M/F, common, father/son, only 1 dominant allele to show trait vs only males, no father/son vs both M/F but more F, no father/son, fathers can pass to daughters

Question 59

autosomal recessive d/o vs consanguinity vs autosomal dom vs assortative mating

Answer 59

you inherit 2 mutated genes (1 from each parent) vs conseq of consanguineous mating that inc chance of recessive dz w/in fam vs you inherit 1 mutated allele vs form of sexual selection where individuals w/ similar phenotypes mate w/ another at a higher rate than expected (even tho it was random)

Question 60

penetrance vs variable expressivity vs locus heterogeneity vs allelic heterogeneity

Answer 60

probability that ppl w/ a mutant allele will actually express that associated trait/dz; ex: Treacher-Collins syndrome, split-hand deformity vs degree of expression of a phenotype from same genotype; CF, Emery-Dreifuss muscular dystrophy vs mutations at mult genes from single or mult chrms can produce same phenotype and each mutation = sufficient to cause dz independently vs different alleles/variants of single gene can cause same/similar dz

Question 61

examples of auto rec vs dom dz

Answer 61

Tay-Sachs dz (defic in HexA enzyme), PKU (defic in phe hydroxylase enzyme --> can't metab phe into tyr), sickle cell, CF, cartilage- hair hypoplasia dwarfism vs achondroplasia, Marfan syndrome (connective tissue d/o), brachydactyly, Huntington's dz

Question 62

examples of x-linked recessive vs dominant d/o

Answer 62

Duchemme muscular trophy: thigh atrophy/bigger calves, paralysis, infertile, death; hemophilia dz affecting Factor IX vs hypophosphatemia, Incontentia pigmenti (F w/ x linked dom w/ mosaic pattern b/c nml X chrm = inactivated; lethal in males)

Question 63

common sxs of mito dz

Answer 63

poor growth, muscle weakness, vision problems, heart/liver/kidney dz, neuro problems; no cures for mito dz

Question 64

homoplasmy vs heteroplasmy

Answer 64

all copies of mtDNA in a euk cell = identical vs copies of mtDNA in a euk cell = diff from e/o

Question 65

myoclonic epilepsy w/ ragged red fibers (MERRF)

Answer 65

mito tRNA mutated --> myoclonus, epilepsy, ataxia, dementia

Question 66

leigh syndrome

Answer 66

severe neuro d/o by progressive loss of mental and movement problems; involved in nuclear AND mito DNA; sxs: N/V, difficulty swallowing/dysphagia, fail to thrive; death by 2-3 yo

Question 67

Chromosome Territory vs Transcpxn Factory

Answer 67

hypothetical compartment where most of a chromosome resides in a highly condensed state and no genes are expressed vs protein machinery required for DNA transcpxn; when you need to transcribe a gene --> loop gene out of chm territory to transcpxn factory

Question 68

CTCF (CCCTC-binding factor) vs cohesin

Answer 68

CTCF binds to certain site along the chromosome and serves as a blocking point and anchors loops vs DNA loops through cohesin circles. CTCF interacts with cohesin to stop the extrusion of DNA and control the size of the chromosomal loops

Question 69

Levels of gene expression regulation

Answer 69

1: directing DNA loops out of chrm territory and to transcpxn factory 2: nucleosome/nucleosome code mod - TF binds to promoter --> histone tails = modified around gene of interest --> some nucleosomes = removed or repositioned to allow more access to DNA helix for other proteins involved in the regulation of gene expression

Question 70

Steps of transcpxn

Answer 70

1) initiation: TFs bind to cis elements and interact w/ pre-initiation complex; TATA binding protein bind to TATA box within promoter region --> guides RNA Polymerase II to TATA in promoter; regulate by proximal/distal promoter elements 2) elongation: unwinds DNA via helicase, relieve torsional stress via topoisomerase, and make pre-mRNA aka heterogenous nuclear RNA (hnRNA) via RNA polymerase; CTD influences elongation. Transcpxn doesn’t require primers 3) termination: release factor disrupts RNA/ribosome complex 4) CTD recruits spliceosome composed of snRNA and snRNPs to splice introns out (though sometimes pre-mRNA doesn’t always have introns) 5) mRNA = cleaved --> 5’ guanine cap added and 3’ poly A tail added to maximize stability when mRNA leaves nucleus to cytosol for transln 6) RNA editing - creates specific protein sequences from an RNA that didn’t encode a functional protein

Question 71

3 diff RNA pol = involved w/ transcpxn and each have diff transcpxn complexes

Answer 71

Pre-Initiation Complexes that must be assembled right on core promoter before transcription can begin; after last subunit comes in => transpxn complex

Question 72

upstream control elements: proximal control elements vs distal control elements

Answer 72

TATA box = not universal. CAAT box and GC box found in very strong promoter further upstream from core promoter; operate just on one gene vs operate in both directions --> affects more than one gene Pol I and Pol III promoters do not have many upstream control elements as they control the transcription of genes that are expressed in all cells at all times. Pol II promoters have more regulation as the genes they direct as expressed in very controlled situations

Question 73

promoter proximal elements/elements of the Core Promoter vs promoter distal elements

Answer 73

upstream DNA seq influencing promoter activity vs includes enhancers, silencers, or insulators (cis elements that stimulate transcription vs cis elements that shut down transcription vs create a boundary between one gene and the next to prevent the histone code from one region to stray into a neighboring region and influence the expression of neighboring genes)

Question 74

cis elements vs trans-acting/transcpxn factors

Answer 74

DNA sequences that define where transcription factors can bind; can by unavail if not in transcpxn factory or if they're held tightly --> can't bind to transcpxn factors vs protein components that bind to these elements; can stimulate or repress the initiation of transcription by interacting w/ pre-initiation complex

Question 75

focused/sharp type vs dispersed/broad type promoters

Answer 75

start at same place same time vs start in general vicinity. both = based on how the pre-initiation complex is assembled to position RNA pol and what promoter elements were used

Question 76

CTD

Answer 76

w/in largest subunit of RNA pol; can by phosphorylated or glycosylated --> D determines what protein partners bind to the advancing polymerase and influence activities.

Question 77

synonymous mutation vs non-synonymous mutation

Answer 77

does not change the amino acid sequence (silent mutation) vs does change the amino acid sequence (nonsense, missense, frameshift)

Question 78

fxns of 5' guanine cap vs polyA tail

Answer 78

protects the RNA from degradation by exonuclease vs protects mRNA from 3’ exonuclease digestion, interacts with the cap to circularize the mRNA, facilitates interaction with the ribosome

Question 79

guide RNAs

Answer 79

guides modification of ribosomal RNAs, polymerization of telomeres, and cleavage and polyadenylation of mRNAs

Question 80

spinal muscular atrophy vs hutchinson-gilford progeria syndrome vs myotonic dystrophy

Answer 80

mutation in SMN1 gene (SMN = used for snRNP synthesis) --> SMN2 gene destroys splicing enhancer and creates splicing silencer --> deficient SMN protein --> degeneration of motor neurons vs muttaion in lamin A/C gene --> incorrect splicing --> truncated protein --> can't be post-modified --> premature aging vs expansions in genes have high affinity to splicing factor MBNL1, but if you deplete MBNL1 --> disrupt alt splicing --> myopathy/tonia, cardiac defects

Question 81

where are ribosomes found?

Answer 81

almost everywhere in cell even in nucleus

Question 82

untranslated region (UTR)

Answer 82

contains sequences that assist in binding to the ribosome and regulate translation

Question 83

charged tRNA

Answer 83

amino acid covalently attached to the 3’ end of the tRNA via Aminoacyl-tRNA synthetase (requires ATP) --> is primed for translation. two step process: amino acid is first attached to an AMP molecule, and then transferred to one of the tRNAs for that amino acid => second genetic code

Question 84

Describe EPA sites

Answer 84

Aminoacyl - tRNA + aa (charged tRNA) comes in Peptidyl - where peptide builds up via peptide bonds Exit - where free tRNA leaves

Question 85

Steps of transln

Answer 85

1) initiating tRNA+met binds to small 40S ribosomal unit —> 40S binds to 5’ cap --> 40S scans along mRNA till it reaches start codon --> large 60S ribosomal unit binds to mRNA; OR ribosome binds to internal ribosome entry site (IRES) of mRNA and start transln w/o looking for start codon (used for translating 2nd open reading frame) 2) ribosome moves in 5’ to 3’ direction and starts adding bases from start codon 3) translation continues till it reaches stop codon. tRNA doesn’t have an anticodon when reaching stop codon --> release factor protein aka eukaryotic translation termination factor 1 (ETF1) binds to stop codon and disrupts ribosome/mRNA complex and releases polypeptide

Question 86

selenocysteine aa

Answer 86

found in active site of detoxifying enzymes; Selenocysteine tRNA is initially charged with serine, which is modified and then replaced with selenocysteine. RNA seq encoding selenocysteine has hairpin structure --> selenocysteine cis element (SECIS) interacts with ribosome to facilitate binding of selenocysteine tRNA.

Question 87

proper protein folding = dependent on?

Answer 87

partially dependent on the amino acid sequence (encoded in the genome) and partially upon a network of helper molecules that prevent the accumulation of poorly folded and thus nonfunctional proteins

Question 88

tert folding = determined by?

Answer 88

hydrophobic interactions, ionic interaction with cations, some electrostatic interactions between charged amino acids like H bonds, and disulfide bonds

Question 89

chaperones

Answer 89

help correctly fold newly synthesized proteins via ATP => foldase; bind to folding intermediates to prevent aggregation => holdase; shuttle polypeptides to a place where they complete assembly => "escort", bind misfolded proteins and escort them to proteasome for degradation; and target aggregates to larger digestive organelles

Question 90

aa seq determines where protein will end up in cell. describe 1st post translational mod

Answer 90

signaling recognition particle (SRP) binds to signal seq/peptide --> escorted to SRP receptor in ER --> docked and transln cont --> polypeptide = injected into ER lumen --> when done translating, signal seq cleaves off

Question 91

fates of proteins translated in ER lumen or its membrane

Answer 91

can mature in ER or golgi

Question 92

fxns of proteolysis

Answer 92

activate a protein, deactivate a protein once it completed its job, portion of the translated polypeptide = removed to create the final protein, a protein has one job until an enzymatic cleavage cuts the protein releasing a frag that has a completely different role in the cell

Question 93

fxns of phosphorylation

Answer 93

activation or inactivation of a protein; major sites = ser, thr, tyr (but other aa can be phosphorylated)

Question 94

fxns of glycosylation

Answer 94

found on secreted proteins and membrane bound proteins; regulation of cell-to-cell binding; target proteins to specific sites in the cell, like the lysosome (branched sugar = attached to polypeptide and cont transln --> moves to Golgi --> N-acetylglucosamine phosphate is added to the terminal mannose residues --> N-acetylglucosamine = removed to leave phosphorylated terminal mannose residues --> protein binds to receptors w/ mannose 6 phosphate marker --> goes to transport vesicle --> fuse w/ endosome and drop cargo --> endosome becomes lysosome containing hydrolytic enzymes; In the absence of mannose phosphorylation, the enzyme is secreted into the extracellular space instead of lysosome (lack of lysosomes --> structural defects in cells)

Question 95

p53 post-translational modification:

Answer 95

deregulated in tumorigenesis

Question 96

fxns of lipidation

Answer 96

target proteins to membranes in organelles (endoplasmic reticulum [ER], Golgi apparatus, mitochondria), vesicles (endosomes, lysosomes) and the plasma membrane by inc hydrophobicity --> inc affinity to membranes; 4 types: C-terminal glycosyl phosphatidylinositol (GPI) anchor, N-terminal myristoylation, S-myristoylation, S-prenylation

Question 97

Mito fxn depends on?

Answer 97

Nuclear and mito DNA

Question 98

Human Genome Project goals

Answer 98

determine seq of 3.2b bases that make up human DNA, identify all genes in human DNA, compile comprehensive polymorphism databases, develop tools for data analysis, fostering biotech innovation, address legal/ethical/social issues that arise from genome research

Question 99

Human Genome Project reference genome

Answer 99

composite genome from several diff ppl; generated from 10-20 primary samples from anon donors across racial and ethnic groups

Question 100

largest gene vs largest protein

Answer 100

dystrophin/DMD gene at 2.4Mb; mutations cause muscular dystrophy vs titin/TTN b/c most exons

Question 101

pseudogenes

Answer 101

genes lost d/t mutations in evolution --> can tell us how we evolved

Question 102

ncRNA vs siRNA

Answer 102

transcribed into RNA but not translated into protein vs involved in gene regulation by binding to mRNA

Question 103

2 classes of transposable/mobile elements

Answer 103

retrotransposons/Class I that break into LTR retrotransposons like retroviruses or non-LTR retrotransposons like LINES/SINES vs DNA transposons/Class II

Question 104

retrotransposons/Class I vs DNA transposons/Class II

Answer 104

copy and paste mechanism --> mutagenic; use reverse transcriptase vs cut/paste mechanism; use transposase

Question 105

LTR retrotransposons vs non-LTR retrotransposons

Answer 105

endogenous retroviruses, retroviral genomes integrated in vertebrates, decayed relic of viruses vs LINEs (long interspersed nuclear elements), contain RT, probs involved in transposition, LINE-1 = most abundant human LINE (516k copies), 6.1kb long; SINEs (short interspersed nuclear elements), don't have RT but can borrow it from retroelements, Alu = most abundant human SINE (>1mil copies), 300bp long

Question 106

minisatellite vs microsatellite

Answer 106

10-100s bps, can be VNTR, can be used in forensics vs <10 bps, like telomere seq TTAGGG. both can expand or contract (contract in humans), both prone to mutations b/c DNA pol slips off --> loops --> returns to work

Question 107

anticipation

Answer 107

dz inc in age of onset in successive generations --> children have more severe form than parents

Question 108

Huntington's dz

Answer 108

nml rpt = 9-29; adult mutation = >40, juvenile mutation >60; sxs: mood change, motor abnormalities mid-life (30/40s) --> involuntary twitching, loss of cognition --> death